1. "That's not what I meant. What I was meaning to say was..."
However, it is probably more common to say "What I meant to say is ..."
This is used after you've said something and you can tell by the response of the hearer that they have misunderstood you.
2. If someone doesn't understand something you are attempting to explain, you may want to restate your sentence and begin by saying, "What I mean is that..."
3. If someone were to ask you what something means you would answer them. "It means that..."
Please, let me know if this helps you.
Interested in Language